rs746982412
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001458.5(FLNC):c.6727+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000097 in 1,453,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001458.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.6727+7A>G | splice_region_variant, intron_variant | ENST00000325888.13 | |||
FLNC-AS1 | NR_149055.1 | n.103-826T>C | intron_variant, non_coding_transcript_variant | ||||
FLNC | NM_001127487.2 | c.6628+7A>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.6727+7A>G | splice_region_variant, intron_variant | 1 | NM_001458.5 | P3 | |||
FLNC | ENST00000346177.6 | c.6628+7A>G | splice_region_variant, intron_variant | 1 | A1 | ||||
FLNC-AS1 | ENST00000469965.1 | n.103-826T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 6AN: 152226Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.00000839 AC: 2AN: 238418Hom.: 0 AF XY: 0.00000766 AC XY: 1AN XY: 130586
GnomAD4 exome AF: 0.0000970 AC: 141AN: 1453704Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 78AN XY: 722494
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
FLNC-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at